Chain-table selection wrong when residue numbering is non-monatonic

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-18)
Description
Click the chain A link in the chain information table for 6pt2 does not select anything.  It uses the command select /A:999-329 apparently because 6pt2 has very weird non-monatonic residue numbering.

Log:
UCSF ChimeraX version: 0.91 (2019-12-18)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6pt2 format mmCIF fromDatabase pdb

6pt2 title:  
Crystal structure of the active δ opioid receptor in complex with the peptide
agonist KGCHM07 [more info...]  
  
Chain information for 6pt2 #1  
---  
Chain | Description  
A B | δ opioid receptor  
C D | Peptide agonist KGCHM07  
  
Non-standard residues in 6pt2 #1  
---  
CLR — cholesterol  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
OXJ — 1-[3,5-bis(trifluoromethyl)phenyl]-N-methylmethanamine  
  
  

> delete /B,D

> delete :999-1106

> select :128

8 atoms, 7 bonds, 1 model selected  

> show sel atoms

> addh

Summary of feedback from adding hydrogens to 6pt2 #1  
---  
warnings | Not adding hydrogens to /A LYS 79 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 81 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 251 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASP 253 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 254 CB because it is missing heavy-atom bond
partners  
1 messages similar to the above omitted  
notes | Termini for 6pt2 (#1) chain A determined from SEQRES records  
Termini for 6pt2 (#1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /C DI7 1  
Chain-initial residues that are not actual N termini: /A ARG 41  
Chain-final residues that are actual C termini: /C OXJ 5  
Chain-final residues that are not actual C termini: /A PHE 329  
300 hydrogen bonds  
Adding 'H' to /A ARG 41  
/A PHE 329 is not terminus, removing H atom from 'C'  
2511 hydrogens added  
  

> help hbond

> hbonds :EJ4

Atom specifier selects no atoms  

> hbonds /C

6 hydrogen bonds found  

> hbonds /C distSlop 0.6

7 hydrogen bonds found  

> hbonds /C distSlop 0.8

7 hydrogen bonds found  

> usage swapaa

swapaa residues resType [angleSlop a number] [bfactor a number] [criteria
criteria] [density a density map specifier] [distSlop a number]
[hbondAllowance a number] [ignoreOtherModels true or false] [lib lib] [log
true or false] [preserve preserve] [relax true or false] [retain true or
false] [scoreMethod scoreMethod] [overlapCutoff a number]  
— Swap amino acid side chain(s)  
resType: a text string  
criteria: some an integer ≥ 0 or a text string  
lib: one of Dunbrack, Dynameomics, Richardson.common, or Richardson.mode  
preserve: a number ≥ 0  
scoreMethod: one of num or sum

swapaa interactive residues resType [lib lib]  
— Show possible side-chain rotamers  
resType: a text string  
lib: one of Dunbrack, Dynameomics, Richardson.common, or Richardson.mode

swapaa mousemode residues restype  
— Replace residue with specified amino acid  
restype: one of ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS,
MET, PHE, PRO, SER, THR, TRP, TYR, or VAL  

> swapaa :128 ASN

Using Dunbrack library  
/A ASP 128: phi -60.7, psi -55.4 trans  
Applying ASN rotamer (chi angles: -73.1 -171.9) to /A ASN 128  

> help swapaa

> swapaa :128 ASP

Using Dunbrack library  
/A ASN 128: phi -60.7, psi -55.4 trans  
Applying ASP rotamer (chi angles: -71.5 -40.2) to /A ASP 128  

> open 6pt2 format mmCIF fromDatabase pdb

6pt2 title:  
Crystal structure of the active δ opioid receptor in complex with the peptide
agonist KGCHM07 [more info...]  
  
Chain information for 6pt2 #2  
---  
Chain | Description  
A B | δ opioid receptor  
C D | Peptide agonist KGCHM07  
  
Non-standard residues in 6pt2 #2  
---  
CLR — cholesterol  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
OXJ — 1-[3,5-bis(trifluoromethyl)phenyl]-N-methylmethanamine  
  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show :128

> hide #!1 models

> close #1

> color :128 & C yellow

> addh

Summary of feedback from adding hydrogens to 6pt2 #2  
---  
warnings | Not adding hydrogens to /A GLU 1008 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 1015 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 1049 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 1059 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 1085 CB because it is missing heavy-atom bond
partners  
49 messages similar to the above omitted  
notes | Termini for 6pt2 (#2) chain A determined from SEQRES records  
Termini for 6pt2 (#2) chain B determined from SEQRES records  
Termini for 6pt2 (#2) chain C determined from SEQRES records  
Termini for 6pt2 (#2) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /C DI7 1, /D DI7 1  
Chain-initial residues that are not actual N termini: /A THR 999, /B ASP 1002,
/B ALA 1023, /B MET 1058, /B ALA 1090, /B ARG 41, /B LYS 250  
Chain-final residues that are actual C termini: /C OXJ 5, /D OXJ 5  
Chain-final residues that are not actual C termini: /A PHE 329, /B GLU 1018,
/B LYS 1042, /B LEU 1078, /B LYS 1104, /B ARG 244, /B CYS 333  
738 hydrogen bonds  
Adding 'H' to /A THR 999  
Adding 'H' to /B ASP 1002  
Adding 'H' to /B ALA 1023  
Adding 'H' to /B MET 1058  
Adding 'H' to /B ALA 1090  
2 messages similar to the above omitted  
/A PHE 329 is not terminus, removing H atom from 'C'  
/B GLU 1018 is not terminus, removing H atom from 'C'  
/B LYS 1042 is not terminus, removing H atom from 'C'  
/B LEU 1078 is not terminus, removing H atom from 'C'  
/B LYS 1104 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
6107 hydrogens added  
  

> hbonds /C distSlop 0.6

7 hydrogen bonds found  

> color /C & C pink

> set bgColor white

> graphics silhouettes true

> save /Users/goddard/Desktop/image1.png supersample 3

> swapaa :128 ASN

Using Dunbrack library  
/A ASP 128: phi -60.7, psi -55.4 trans  
/B ASP 128: phi -61.8, psi -47.2 trans  
Applying ASN rotamer (chi angles: -73.1 -171.9) to /A ASN 128  
Applying ASN rotamer (chi angles: -175.1 112.2) to /B ASN 128  

> save /Users/goddard/Desktop/image1.png supersample 3

> close

> open https://www.rbvi.ucsf.edu/chimerax/data/delta-opioid-
jan2020/binding.html

Opened 'https://www.rbvi.ucsf.edu/chimerax/data/delta-opioid-
jan2020/binding.html' in browser  

> open 6ddf

6ddf title:  
μ Opioid Receptor-Gi Protein Complex [more info...]  
  
Chain information for 6ddf #1  
---  
Chain | Description  
A | Guanine nucleotide-binding protein G(i) subunit alpha-1  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2  
D | DAMGO  
R | Mu-type opioid receptor  
  
Non-standard residues in 6ddf #1  
---  
ETA — ethanolamine  
  
  

> set bgColor black

> close

> open 4n6h

4n6h title:  
1.8 A Structure of the human δ opioid 7TM receptor (PSI Community Target)
[more info...]  
  
Chain information for 4n6h #1  
---  
Chain | Description  
A | Soluble cytochrome b562, Delta-type opioid receptor chimeric protein  
  
Non-standard residues in 4n6h #1  
---  
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)  
NA — sodium ion  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
PGE — triethylene glycol  
TLA — L(+)-tartaric acid  
  
  

> surface

> mlp

Map values for surface "4n6h_A SES surface": minimum -26.77, mean -0.8566,
maximum 23.81  

> lighting soft

> lighting simple

> hide surfaces

> delete :1002-1106

> hbonds

581 hydrogen bonds found  

> hbonds ligand

40 hydrogen bonds found  

> hbonds :EJ4

10 hydrogen bonds found  

> color :EJ4 orange

> color byhetero

> hide cartoons

> clip off

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide atoms

> show :EJ4 :< 4

> addh

Summary of feedback from adding hydrogens to 4n6h #1  
---  
warnings | Not adding hydrogens to /A ARG 41 CD because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A VAL 154 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LEU 157 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 166 CE because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 192 CD because it is missing heavy-atom bond
partners  
10 messages similar to the above omitted  
notes | Termini for 4n6h (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 36  
Chain-final residues that are actual C termini: /A GLY 338  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLY 338  
580 hydrogen bonds  
Adding 'H' to /A GLY 36  
3076 hydrogens added  
  

> open 4n6h fromDatabase eds

Opened 4n6h.ccp4, grid size 114,100,190, pixel 0.599,0.607,0.603, shown at
level 0.799, step 1, values float32  

> volume zone #2 nearAtoms :EJ4 range 6 newMap false

> volume #2 level 0.3259

> delete H

> volume #2 level 0.6317

> volume #2 level 0.3951

> volume #2 level 0.2047

> volume #2 level 0.6259

> volume level .5

> close #2

> style :EJ4 sphere

Changed 31 atom styles  

> surface :EJ4 :< 4

> transparency 50

> open 6pt2

6pt2 title:  
Crystal structure of the active δ opioid receptor in complex with the peptide
agonist KGCHM07 [more info...]  
  
Chain information for 6pt2 #2  
---  
Chain | Description  
A B | δ opioid receptor  
C D | Peptide agonist KGCHM07  
  
Non-standard residues in 6pt2 #2  
---  
CLR — cholesterol  
OLA — oleic acid  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
OXJ — 1-[3,5-bis(trifluoromethyl)phenyl]-N-methylmethanamine  
  
  

> hide #1 models

> view

> select #2/A:999-329

Nothing selected  




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

"/A & (protein | nucleic)" is close, but would pick up peptide ligands. Maybe also " & ~ligand"?

Can (non-standard) structures have multiple chains with the same ID? Need to review the code.